| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:38 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the puma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/puma.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1554/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| puma 3.43.0 (landing page) Xuejun Liu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: puma |
| Version: 3.43.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:puma.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings puma_3.43.0.tar.gz |
| StartedAt: 2023-05-10 01:08:21 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 01:17:37 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 556.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: puma.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:puma.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings puma_3.43.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/puma.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.43.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘puma’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘oligoClasses’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’
‘oligo:::probeNames’ ‘oligo:::rma’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMmmgmos: no visible binding for global variable ‘median’
PMmmgmos: no visible global function definition for ‘description’
calcAUC: no visible global function definition for ‘prediction’
calcAUC: no visible global function definition for ‘performance’
calculateLimma: no visible global function definition for ‘lmFit’
calculateLimma: no visible global function definition for
‘contrasts.fit’
calculateLimma: no visible global function definition for ‘eBayes’
calculateTtest : <anonymous>: no visible global function definition for
‘t.test’
clusterApplyLBDots : submit: no visible global function definition for
‘sendCall’
clusterApplyLBDots: no visible global function definition for
‘recvOneResult’
clusterNormE: no visible global function definition for ‘var’
clusterNormVar: no visible global function definition for ‘var’
compareLimmapumaDE: no visible global function definition for ‘pdf’
compareLimmapumaDE: no visible global function definition for ‘dev.off’
compareLimmapumaDE: no visible global function definition for ‘par’
compareLimmapumaDE: no visible global function definition for
‘vennDiagram’
createDesignMatrix: no visible global function definition for
‘model.matrix’
erfc: no visible global function definition for ‘pnorm’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘data’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmhta: no visible binding for global variable ‘median’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘data’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
gmoExon: no visible binding for global variable ‘median’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘read.table’
igmoExon: no visible global function definition for ‘data’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible binding for global variable ‘median’
just.mgmos: no visible binding for global variable ‘median’
just.mmgmos: no visible binding for global variable ‘median’
legend2: no visible global function definition for ‘par’
legend2: no visible global function definition for ‘xy.coords’
legend2 : rect2: no visible global function definition for ‘rect’
legend2 : segments2: no visible global function definition for
‘segments’
legend2 : points2: no visible global function definition for ‘points’
legend2 : text2: no visible global function definition for ‘text’
legend2: no visible global function definition for ‘strwidth’
legend2: no visible global function definition for ‘xinch’
legend2: no visible global function definition for ‘yinch’
legend2: no visible global function definition for ‘strheight’
matrixDistance: no visible global function definition for ‘dist’
mgmos: no visible binding for global variable ‘median’
mmgmos: no visible binding for global variable ‘median’
plot.pumaPCARes: no visible global function definition for ‘text’
plot.pumaPCARes: no visible global function definition for ‘legend’
plotErrorBars: no visible global function definition for ‘qnorm’
plotErrorBars: no visible global function definition for ‘par’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotErrorBars: no visible global function definition for ‘arrows’
plotErrorBars: no visible global function definition for ‘points’
plotErrorBars: no visible global function definition for ‘axis’
plotErrorBars: no visible global function definition for ‘title’
plotHistTwoClasses: no visible global function definition for ‘axis’
plotHistTwoClasses: no visible global function definition for ‘box’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
plotWhiskers: no visible global function definition for ‘segments’
plotWhiskers: no visible global function definition for ‘qnorm’
plotWhiskers: no visible global function definition for ‘points’
plotWhiskers: no visible global function definition for ‘abline’
pumaClust: no visible global function definition for ‘read.csv’
pumaClust: no visible global function definition for ‘kmeans’
pumaClust: no visible global function definition for ‘cov’
pumaClustii: no visible global function definition for ‘read.csv’
pumaClustii: no visible global function definition for ‘cov’
pumaComb: no visible global function definition for ‘getMPIcluster’
pumaComb: no visible global function definition for ‘makeCluster’
pumaComb: no visible global function definition for ‘clusterEvalQ’
pumaComb: no visible global function definition for ‘clusterApplyLB’
pumaCombImproved: no visible global function definition for
‘getMPIcluster’
pumaCombImproved: no visible global function definition for
‘makeCluster’
pumaCombImproved: no visible global function definition for
‘clusterEvalQ’
pumaCombImproved: no visible global function definition for
‘clusterApplyLB’
pumaFull: no visible global function definition for ‘pdf’
pumaFull: no visible global function definition for ‘par’
pumaFull: no visible global function definition for ‘prcomp’
pumaFull: no visible global function definition for ‘dev.off’
pumaNormalize: no visible binding for global variable ‘median’
pumaPCA: no visible global function definition for ‘prcomp’
pumaPCA: no visible global function definition for ‘rnorm’
pumaPCA: no visible global function definition for ‘optimise’
pumaPCA: no visible global function definition for ‘optim’
pumaPCA: no visible global function definition for ‘par’
pumaPCARemoveRedundancy: no visible global function definition for
‘dist’
write.reslts,DEResult: no visible global function definition for
‘write.table’
write.reslts,ExpressionSet: no visible global function definition for
‘write.table’
write.reslts,exprReslt: no visible global function definition for
‘write.table’
write.reslts,pumaPCARes: no visible global function definition for
‘write.table’
Undefined global functions or variables:
abline arrows axis box clusterApplyLB clusterEvalQ contrasts.fit cov
data description dev.off dist eBayes even getMPIcluster kmeans legend
lmFit makeCluster median model.matrix odd optim optimise par pdf
performance pnorm points prcomp prediction qnorm read.csv read.table
rect recvOneResult rnorm segments sendCall stopCluster strheight
strwidth t.test text title var vennDiagram write.table xinch
xy.coords yinch
Consider adding
importFrom("grDevices", "dev.off", "pdf", "xy.coords")
importFrom("graphics", "abline", "arrows", "axis", "box", "legend",
"par", "points", "rect", "segments", "strheight",
"strwidth", "text", "title", "xinch", "yinch")
importFrom("stats", "cov", "dist", "kmeans", "median", "model.matrix",
"optim", "optimise", "pnorm", "prcomp", "qnorm", "rnorm",
"t.test", "var")
importFrom("utils", "data", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) DEResult-class.Rd:92: Escaped LaTeX specials: \_
checkRd: (-1) DEResult-class.Rd:93: Escaped LaTeX specials: \_
checkRd: (-1) PMmmgmos.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) PMmmgmos.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) createContrastMatrix.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) exprReslt-class.Rd:100: Escaped LaTeX specials: \_
checkRd: (-1) exprReslt-class.Rd:101: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) exprReslt-class.Rd:102: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) gmhta.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) gmoExon.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hcomb.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) hcomb.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) igmoExon.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) justmgMOS.Rd:41: Escaped LaTeX specials: \_ \_
checkRd: (-1) justmmgMOS.Rd:41: Escaped LaTeX specials: \_ \_
checkRd: (-1) legend2.Rd:134: Escaped LaTeX specials: \&
checkRd: (-1) mgmos.Rd:25: Escaped LaTeX specials: \_ \_
checkRd: (-1) mgmos.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) mmgmos.Rd:26: Escaped LaTeX specials: \_ \_
checkRd: (-1) mmgmos.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) mmgmos.Rd:38: Escaped LaTeX specials: \_
checkRd: (-1) pumaFull.Rd:23: Escaped LaTeX specials: \_ \_
checkRd: (-1) pumaFull.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) pumaFull.Rd:25: Escaped LaTeX specials: \_ \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
puma-package 39.884 0.468 40.353
pumaDE 25.071 0.228 25.301
pumaCombImproved 15.372 0.160 15.533
pumaComb 10.740 0.100 10.841
pumaclust 7.794 0.008 7.802
plot-methods 7.400 0.280 7.679
pumaPCA 6.537 0.124 6.661
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘puma.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/puma.Rcheck/00check.log’
for details.
puma.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL puma ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘puma’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c PMmultimgmos.c -o PMmultimgmos.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c cregistration.c -o cregistration.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c donlp2.c -o donlp2.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c gme.c -o gme.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ipplr_c.c -o ipplr_c.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c multimgmos.c -o multimgmos.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c newx.c -o newx.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pplr_c.c -o pplr_c.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pumaclust_c.c -o pumaclust_c.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c user_eval.c -o user_eval.o gcc -shared -L/usr/local/lib -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-puma/00new/puma/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (puma)
puma.Rcheck/puma-Ex.timings
| name | user | system | elapsed | |
| DEResult-class | 0.001 | 0.000 | 0.001 | |
| PMmmgmos | 0 | 0 | 0 | |
| bcomb | 0 | 0 | 0 | |
| calcAUC | 0 | 0 | 0 | |
| calculateFC | 0.000 | 0.000 | 0.001 | |
| calculateLimma | 0 | 0 | 0 | |
| calculateTtest | 0 | 0 | 0 | |
| clusterNormE | 0 | 0 | 0 | |
| clusterNormVar | 0 | 0 | 0 | |
| createContrastMatrix | 0.017 | 0.001 | 0.019 | |
| createDesignMatrix | 0.025 | 0.000 | 0.025 | |
| erfc | 0.001 | 0.000 | 0.000 | |
| exprReslt-class | 0 | 0 | 0 | |
| gmhta | 0.000 | 0.000 | 0.001 | |
| gmoExon | 0 | 0 | 0 | |
| hcomb | 0 | 0 | 0 | |
| igmoExon | 0.001 | 0.000 | 0.000 | |
| legend2 | 0.001 | 0.000 | 0.000 | |
| license.puma | 0.002 | 0.000 | 0.001 | |
| matrixDistance | 0 | 0 | 0 | |
| mgmos | 0.001 | 0.000 | 0.000 | |
| mmgmos | 0 | 0 | 0 | |
| normalisation.gs | 0.000 | 0.000 | 0.001 | |
| numFP | 0 | 0 | 0 | |
| numOfFactorsToUse | 0 | 0 | 0 | |
| numTP | 0.001 | 0.000 | 0.000 | |
| orig_pplr | 0.001 | 0.000 | 0.000 | |
| plot-methods | 7.400 | 0.280 | 7.679 | |
| plotErrorBars | 0.287 | 0.004 | 0.292 | |
| plotHistTwoClasses | 0.01 | 0.00 | 0.01 | |
| plotROC | 0 | 0 | 0 | |
| pplr | 0.154 | 0.008 | 0.162 | |
| puma-package | 39.884 | 0.468 | 40.353 | |
| pumaClustii | 3.368 | 0.036 | 3.404 | |
| pumaComb | 10.740 | 0.100 | 10.841 | |
| pumaCombImproved | 15.372 | 0.160 | 15.533 | |
| pumaDE | 25.071 | 0.228 | 25.301 | |
| pumaFull | 0 | 0 | 0 | |
| pumaNormalize | 0.317 | 0.008 | 0.325 | |
| pumaPCA | 6.537 | 0.124 | 6.661 | |
| pumaclust | 7.794 | 0.008 | 7.802 | |
| removeUninformativeFactors | 0.036 | 0.000 | 0.036 | |